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PLoS One. 2019 Jul 24;14(7):e0218407. doi: 10.1371/journal.pone.0218407. eCollection 2019.

Genome-wide SNP analysis of Japanese Thoroughbred racehorses.

Author information

SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa 240-0193, Japan.
RIKEN iTHEMS, Wako, Saitama 351-0198, Japan.
Hidaka Training and Research Center, Japan Racing Association, Hokkaido 057-0171, Japan.
Genetic Analysis Department, Laboratory of Racing Chemistry, Utsunomiya, Tochigi 320-0851, Japan.


The domestication process of plants and animals typically involves intense inbreeding and directional selection for various traits. Here, we genotyped 370 Japanese Thoroughbred horses using the recently developed 670k SNP array and performed various genome-wide analysis also using genotype data of other horse breeds. We identified a number of regions showing interesting patterns of polymorphisms. For instance, the region containing the MC1R locus associated with chestnut coat color may have been targeted by selection for a different mutation much earlier on than the recent selection for chestnut color. We also identified regions that show signatures of selection specific to Thoroughbreds. In addition, we found that intense inbreeding early in the history of the Thoroughbred breed and also before the formation of the breed has a significant impact on the genomic architecture of modern Thoroughbreds. Our study demonstrates that the horse 670k array can be utilized to gain important insight into the domestication process of horses and to understand the genetic basis of the phenotypic diversity in horses.

Conflict of interest statement

FS is an employee of Hidaka Training and Research Center, Japan Racing Association; TT is an employee of Genetic Analysis Department, Laboratory of Racing Chemistry. This does not alter our adherence to PLOS ONE policies on sharing data and materials. All other authors declare that no competing interests exist.

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